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Pull Request Pull Request #112: feat(New hiseqx validation functions)

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68.16

/demux/utils/samplesheet.py

import re

from collections import OrderedDict
from copy import deepcopy
from pathlib import Path
from typing import Tuple

from demux.constants.constants import COMMA, NEW_LINE


class SampleSheetValidationException(Exception):
    def __init__(self, section, msg, line_nr):
        self.section = section
        self.msg = msg
        self.line_nr = line_nr

    def __str__(self):
        return repr(
            "Section '{}', Line '{}': {}".format(self.section, self.msg, self.line_nr)
        )


class SampleSheetParseException(Exception):
    pass


class Line(dict):
    @staticmethod
    def _reverse_complement(dna):
        complement = {"A": "T", "C": "G", "G": "C", "T": "A"}
        return "".join([complement[base] for base in dna[::-1]])

    @property
    def dualindex(self, delim="-", revcomp=False):
        if "index2" in self and len(self["index2"]):
            index2 = (
                self._reverse_complement(self["index2"]) if revcomp else self["index2"]
            )
            return self["index"] + delim + index2
        return self["index"]


class Samplesheet(object):
    """SampleSheet.

    Stores the samplesheet in sections: self.section
    e.g. [Data] section will be stored in self.section['[Data]']

    The [Data] section is the actual samplesheet. It consists of a '[Data]' section marker,
    a column header, and the rows of samplesheet data.

    This will be split on line, with each line turned into a dictionary (column header as keys),
    and stored into self.samplesheet.

    e.g.:

    [Data],,
    Flowcell,SampleID,Index
    HHGGFFSS,ADM1123A1,ACTGACTG

    self.section['[Data]'] = [
        {'FCID': 'HHGGFFSS', 'SampleID': 'ADM1123A1', 'Index': 'ACTGACTG'}
    ]

    The original split line with the section marker, will be stored in self.section_markers['[Data]'] = ['[Data]','','']

    """

    # known sections
    HEADER = "[Header]"
    DATA = "[Data]"

    # for the [Data] section: provide a universal header line.
    # The mapping is like this: universal: expected, e.g. for NIPT we have expected Sample_ID,
    # which is mapped to the more universal 'sample_id': 'sample_id': 'Sample_ID'
    # Universal keys follow the python variable naming rules:
    # lowercase with words separated by underscores as necessary to improve readability.
    # One can make one header map for each samplesheet type.
    header_map = {
        "fcid": "FCID",
        "lane": "Lane",
        "sample_id": "SampleID",
        "sample_ref": "SampleRef",
        "index": "index",
        "index2": "index2",
        "sample_name": "SampleName",
        "control": "Control",
        "recipe": "Recipe",
        "operator": "Operator",
        "project": "Project",
    }

    def _get_flowcell(self):
        for line in self.section[self.DATA]:
            if "Flowcell" in line:
                return line["Flowcell"]
        return None

    def __init__(self, samplesheet_path):
        self.samplesheet_path = samplesheet_path
        self.original_sheet = []  # all lines of the samplesheet
        self.section_markers = (
            dict()
        )  # [Name]: line; does this section have a named section
        self.parse(samplesheet_path)

    def _get_data_header(self):
        header_r = self._get_data_header_r()
        header_map_r = dict((v, k) for k, v in self.header_map.items())
        header = [header_map_r[k] for k in header_r]

        return header

    def _get_data_header_r(self):
        return self.section[self.DATA][0]

    def _get_header_key(self, key):
        if key not in self.header_map:
            raise KeyError("'{}' not in header_map!".format(key))
        return self.header_map[key]

    def parse(self, samplesheet_path, delim=","):
        """
        Parses a Samplesheet, with their fake csv format.
        Should be instantiated with the samplesheet path as an argument.
        Will create a dict for each section. Header: (lines)
        """

        name = "[Data]"
        self.section = OrderedDict()
        with open(samplesheet_path) as csvfile:
            for line in csvfile.readlines():
                line = line.strip()
                line = line.split(delim)
                self.original_sheet.append(line)
                if line[0].startswith("["):
                    name = line[0]
                    self.section_markers[name] = line
                    continue  # skip the actual section header

                if name not in self.section:
                    self.section[name] = []

                self.section[name].append(line)

        if self.DATA not in self.section:
            raise SampleSheetParseException("No data found!")

        header = self._get_data_header()
        self.samplesheet = [
            Line(dict(zip(header, line))) for line in self.section[self.DATA][1:]
        ]

        header_r = self._get_data_header_r()
        self.samplesheet_r = [
            dict(zip(header_r, line)) for line in self.section[self.DATA][1:]
        ]

    def lines(self):
        """ Yields all lines of the [Data] section. """
        for line in self.samplesheet:
            yield line

    def lines_r(self):
        """ Yields all lines of the [Data] section based on the original header """
        for line in self.samplesheet_r:
            yield line

    def raw(self, delim=",", end="\n"):
        """Reconstructs the sample sheet. """
        rs = []
        for line in self.original_sheet:
            rs.append(delim.join(line))
        return end.join(rs)

    def samples(self, column="sample_id"):
        """ Return all samples in the samplesheet """
        return self.column(column)

    def samples_r(self, column="SampleID"):
        """ Return all samples in the samplesheet based on the original header"""
        return self.column_r(column)

    def column(self, column):
        """ Return all values from a column in the samplesheet """
        for line in self.samplesheet:
            yield line[column]

    def column_r(self, column):
        """ Return all values from a column in the samplesheet based on the original header"""
        for line in self.samplesheet_r:
            yield line[column]

    def cell(self, line, column):
        """ return the contents of a column in a line """

        return line[self._get_header_key(column)]

    def lines_per_column(self, column, content):
        """Return all lines with the same column content
        e.g. return all lines of column='lane' content='1'"""
        for line in self.samplesheet:
            if line[column] == content:
                yield line

    def lines_per_column_r(self, column, content):
        """Return all lines with the same column content
        e.g. return all lines of column='Lane' content='1'"""
        for line in self.samplesheet_r:
            if line[column] == content:
                yield line

    def is_pooled_lane(self, lane, column="lane"):
        """ Return True if lane contains multiple samples """
        lane_count = 0
        lane = str(lane)
        for line in self.samplesheet:
            if line[column] == lane:
                lane_count += 1

            if lane_count > 1:
                return True

        return False

    def is_pooled_lane_r(self, lane, column="lane"):
        """ Return True if lane contains multiple samples based on the original header """
        lane_count = 0
        lane = str(lane)
        for line in self.samplesheet_r:
            if line[column] == lane:
                lane_count += 1

            if lane_count > 1:
                return True

        return False

    def validate(self):
        """ General validation of a samplesheet """

        def _validate_length(section):
            if len(section) > 2:
                header = section[0]
                lines = section[1:]
                for i, line in enumerate(lines):
                    if len(header) != len(line):
                        msg = "'{}': #fields != #fields in header".format(line)
                        # add i + 2 as it makes it easier to spot the 'wrong' line
                        return (msg, i + 2)
            return True

        def _validate_unique_index(samplesheet):
            lanes = list(set(self.column("lane")))
            for lane in lanes:
                if self.is_pooled_lane(lane, column="lane"):
                    sample_of = dict()
                    for line in self.lines_per_column("lane", lane):
                        index = line["index"]
                        if index not in sample_of:
                            sample_of[index] = set()
                        sample_of[index].add(line["sample_id"])
                    for index, samples in sample_of.items():
                        if len(samples) > 1:
                            samples_list = list(samples)
                            samples_list.sort()
                            return (
                                "Same index for {} on lane {}".format(
                                    " , ".join(samples_list), lane
                                ),
                                index,
                            )

            return True

        def _validate_sample_name(samplesheet):
            for i, line in enumerate(samplesheet):
                forbidden_chars = set(" ")
                if any((c in forbidden_chars) for c in line["sample_id"]):
                    return (
                        "Sample contains forbidden chars ({}): {}".format(
                            forbidden_chars, line["sample_id"]
                        ),
                        i + 2,
                    )

        rs = _validate_unique_index(self.samplesheet)
        if type(rs) is tuple:
            raise SampleSheetValidationException(self.DATA, rs[1], rs[0])

        for section_marker, section in self.section.items():
            validation_section = section[
                :
            ]  # only validate the content, not the [Data] header
            rs = _validate_length(validation_section)
            if type(rs) is tuple:
                raise SampleSheetValidationException(section_marker, rs[1], rs[0])

        rs = _validate_sample_name(self.samplesheet)
        if type(rs) is tuple:
            raise SampleSheetValidationException(self.DATA, rs[1], rs[0])

        return True


class HiSeqXSamplesheet(Samplesheet):
    def unparse(self, delim=","):
        """Reconstruct the sample sheet based on the (modified) parsed values. """

        yield "[Data]"
        yield delim.join(self._get_data_header_r())
        for line in self.samplesheet:
            line_r = []
            for part in self._get_data_header():
                line_r.append(line[part])
            yield delim.join(line_r)

    def validate(self):
        Samplesheet.validate(self)

        def _validate_project_samplename() -> Tuple[str, int]:
            for i, line in enumerate(self.lines()):
                if line["project"] != line["sample_name"]:
                    # add i + 2 as it makes it easier to spot the 'wrong' line
                    line_nr = i + 2
                    msg = "Project and SampleName cannot be different!"
                    return msg, line_nr

        def _validate_index() -> Tuple[str, int]:
            for i, line in enumerate(self.lines()):
                if line["index"] == "":
                    # add i + 2 as it makes it easier to spot the 'wrong' line
                    line_nr = i + 2
                    msg = "Missing index!"
                    return msg, line_nr

        def _validate_index_types() -> Tuple[str, None]:
            """ Check if there are multiple types of indexes, meaning single, dual, or both """

            indexes = []
            try:
                for index in zip(self.column("index"), self.column("index2")):
                    new_index_type = (len(index[0]), len(index[1]))
                    if not any(
                        [index_type == new_index_type for index_type in indexes]
                    ):
                        indexes.append(new_index_type)
            except KeyError:
                for index in self.column("index"):
                    new_index_type = (len(index[0]), len(index[1]))
                    if not any(
                        [index_type == new_index_type for index_type in indexes]
                    ):
                        indexes.append(new_index_type)
            if len(indexes) > 1:
                msg = "Multiple index types in SampleSheet!"
                line_nr = None
                return msg, line_nr

        for rs in [
            _validate_index(),
            _validate_project_samplename(),
            _validate_index_types(),
        ]:
            if type(rs) is tuple:
                raise SampleSheetValidationException(self.DATA, rs[1], rs[0])

        return True


class iseqSampleSheet(Samplesheet):

    header_map = {
        "fcid": "FCID",
        "sample_id": "Sample_ID",
        "sample_name": "Sample_Name",
        "description": "Description",
        "index": "index",
        "index2": "index2",
        "project": "Sample_Project",
    }


class MiseqSamplesheet(Samplesheet):

    header_map = {
        "lane": "Lane",
        "sample_id": "Sample_ID",
        "sample_name": "Sample_Name",
        "sample_plate": "Sample_Plate",
        "sample_well": "Sample_Well",
        "i7_index_id": "I7_Index_ID",
        "index": "index",
        "sample_project": "Sample_Project",
        "index2": "index2",
        "i5_index_id": "I5_Index_ID",
        "genome_folder": "GenomeFolder",
        "description": "Description",
    }

    si5 = {
        "TAGATCGC": "S501",
        "CTCTCTAT": "S502",
        "TATCCTCT": "S503",
        "AGAGTAGA": "S504",
        "GTAAGGAG": "S505",
        "ACTGCATA": "S506",
        "AAGGAGTA": "S507",
        "CTAAGCCT": "S508",
        "CGTCTAAT": "S510",
        "TCTCTCCG": "S511",
        "TCGACTAG": "S513",
        "TTCTAGCT": "S515",
        "CCTAGAGT": "S516",
        "GCGTAAGA": "S517",
        "CTATTAAG": "S518",
        "AAGGCTAT": "S520",
        "GAGCCTTA": "S521",
        "TTATGCGA": "S522"
        #'TAGATCGC': 'N501',
        #'CTCTCTAT': 'N502',
        #'TATCCTCT': 'N503',
        #'AGAGTAGA': 'N504',
        #'GTAAGGAG': 'N505',
        #'ACTGCATA': 'N506',
        #'AAGGAGTA': 'N507',
        #'CTAAGCCT': 'N508',
    }
    ni7 = {
        "TAAGGCGA": "N701",
        "CGTACTAG": "N702",
        "AGGCAGAA": "N703",
        "TCCTGAGC": "N704",
        "GGACTCCT": "N705",
        "TAGGCATG": "N706",
        "CTCTCTAC": "N707",
        "CAGAGAGG": "N708",
        "CGAGGCTG": "N710",
        "AAGAGGCA": "N711",
        "GTAGAGGA": "N712",
        "GCTCATGA": "N714",
        "ATCTCAGG": "N715",
        "ACTCGCTA": "N716",
        "GGAGCTAC": "N718",
        "GCGTAGTA": "N719",
        "CGGAGCCT": "N720",
        "TACGCTGC": "N721",
        "ATGCGCAG": "N722",
        "TAGCGCTC": "N723",
        "ACTGAGCG": "N724",
        "CCTAAGAC": "N726",
        "CGATCAGT": "N727",
        "TGCAGCTA": "N728",
        "TCGACGTC": "N729",
    }
    di7 = {
        "ATTACTCG": "D701",
        "TCCGGAGA": "D702",
        "CGCTCATT": "D703",
        "GAGATTCC": "D704",
        "ATTCAGAA": "D705",
        "GAATTCGT": "D706",
        "CTGAAGCT": "D707",
        "TAATGCGC": "D708",
        "CGGCTATG": "D709",
        "TCCGCGAA": "D710",
        "TCTCGCGC": "D711",
        "AGCGATAG": "D712",
    }
    di5 = {
        "TATAGCCT": "D501",
        "ATAGAGGC": "D502",
        "CCTATCCT": "D503",
        "GGCTCTGA": "D504",
        "AGGCGAAG": "D505",
        "TAATCTTA": "D506",
        "CAGGACGT": "D507",
        "GTACTGAC": "D508",
    }

    def __init__(self, samplesheet_path, flowcell=None, sequencing_date=None):
        Samplesheet.__init__(self, samplesheet_path)
        if flowcell == None:
            flowcell = Path(samplesheet_path).dirname().basename().split("_")[-1]
        if sequencing_date == None:
            sequencing_date = Path(samplesheet_path).dirname().basename().split("_")[0]
        self.flowcell = flowcell
        self.sequencing_date = sequencing_date

    def _get_flowcell(self):
        return self.flowcell

    def to_demux(self, delim=",", end="\n"):
        """ Convert miseq to hiseq style samplesheet for demultiplexing. """

        checked_indexes = {}  # the indexes in the SampleSheet

        def clean(input):
            return re.sub(r"[ _/]+", "", input)

        def check_index(index):
            checked_indexes[index] = 1

        def get_undetermined_indexes():

            # combine the D indexes
            for di7_index, di7_name in self.di7.items():
                for di5_index, di5_name in self.di5.items():
                    d_index = di7_index + "-" + di5_index
                    if d_index not in checked_indexes:
                        yield d_index, str(di7_name + "-" + di5_name)

            # combine the other indexes
            for ni7_index, ni7_name in self.ni7.items():
                for si5_index, si5_name in self.si5.items():
                    ns_index = ni7_index + "-" + si5_index
                    if ns_index not in checked_indexes:
                        yield ns_index, str(ni7_name + "-" + si5_name)

        expected_header = [
            "FCID",
            "Lane",
            "SampleID",
            "SampleRef",
            "Index",
            "Description",
            "Control",
            "Recipe",
            "Operator",
            "SampleProject",
        ]

        # get the experiment name
        flowcell_id = self._get_flowcell()
        cur_date = self.sequencing_date

        header = self.section[self.DATA][0]  # '0' is the csv header
        data_lines = (
            []
        )  # the new data section. Each line holds a dict with the right header keys
        data_lines.append(expected_header)
        for line in self.samplesheet:
            data_line = {}
            data_line["FCID"] = flowcell_id
            data_line["Lane"] = "1"
            data_line["SampleID"] = cur_date + "-" + clean(line["sample_id"])
            data_line["SampleRef"] = "hg19"
            data_line["Index"] = clean(line["index"]) + "-" + clean(line["index2"])
            data_line["Description"] = line["description"]
            data_line["Control"] = "N"
            data_line["Recipe"] = "R1"
            data_line["Operator"] = "MS"
            data_line["SampleProject"] = clean(line["sample_project"])

            check_index(clean(line["index"]) + "-" + clean(line["index2"]))

            ordered_line = []
            for head in expected_header:
                ordered_line.append(data_line[head])
            data_lines.append(ordered_line)

        # add the undetermined indexes
        for undetermined_index, undetermined_index_name in get_undetermined_indexes():
            data_line = {}
            data_line["FCID"] = flowcell_id
            data_line["Lane"] = "1"
            data_line["SampleID"] = cur_date + "-" + undetermined_index_name
            data_line["SampleRef"] = "hg19"
            data_line["Index"] = undetermined_index
            data_line["Description"] = "ctmr"
            data_line["Control"] = "N"
            data_line["Recipe"] = "R1"
            data_line["Operator"] = "script"
            data_line["SampleProject"] = "Undetermined"

            ordered_line = []
            for head in expected_header:
                ordered_line.append(data_line[head])
            data_lines.append(ordered_line)

        rs = []
        for line in data_lines:
            rs.append(delim.join(line))

        return end.join(rs)

    def validate(self):
        Samplesheet.validate(self)

        def _validate_missing_index():
            """We know what indexes to expect in the samplesheet. Check which ones are missing
            or have been added."""

            def is_readymade_index(index):
                for di7_index, di7_name in self.di7.items():
                    for di5_index, di5_name in self.di5.items():
                        d_index = di7_index + "-" + di5_index
                        if index == d_index:
                            return index

                # combine the other indexes
                for ni7_index, ni7_name in self.ni7.items():
                    for si5_index, si5_name in self.si5.items():
                        ns_index = ni7_index + "-" + si5_index
                        if index == ns_index:
                            return index

            for i, line in enumerate(self.lines()):
                readymade_index = is_readymade_index(line["index"])

                if not readymade_index:
                    return (
                        "Index {} not in readymade indexes!".format(line["index"]),
                        i,
                    )

        rs = _validate_missing_index()
        if type(rs) is tuple:
            raise SampleSheetValidationException(self.DATA, rs[1], rs[0])


class HiSeq2500Samplesheet(Samplesheet):

    header_map = {
        "fcid": "FCID",
        "lane": "Lane",
        "sample_id": "SampleID",
        "sample_ref": "SampleRef",
        "index": "Index",
        "index2": "Index2",
        "sample_name": "SampleName",
        "control": "Control",
        "recipe": "Recipe",
        "operator": "Operator",
        "description": "Description",
        "project": "SampleProject",
    }

    def convert(self, delim: str = COMMA, end: str = NEW_LINE) -> str:
        """Converts an old HiSeq2500 sample sheet for use on Hasta"""

        def _is_dual_index(line: list) -> bool:
            return "Index2" in line

        def _insert_empty_index(line: list) -> None:
            line.insert(5, "")

        converted_samplesheet: list = list()
        converted_samplesheet.append(self.DATA)
        header: list = self.section[self.DATA][0]
        sample_rows: list = self.section[self.DATA][1:]
        new_header: list = list(Samplesheet.header_map.values())
        converted_header: str = delim.join(new_header)
        converted_samplesheet.append(converted_header)

        for row in sample_rows:
            if not _is_dual_index(header):
                _insert_empty_index(row)
            converted_row = delim.join(row)
            converted_samplesheet.append(converted_row)

        return end.join(converted_samplesheet)


class NIPTSamplesheet(Samplesheet):

    header_map = {
        "lane": "Lane",
        "sample_id": "Sample_ID",
        "sample_name": "Sample_Name",
        "sample_plate": "Sample_Plate",
        "sample_well": "Sample_Well",
        "i7_index_id": "I7_Index_ID",
        "index": "index",
        "sample_project": "Sample_Project",
        "description": "Description",
        "sample_type": "SampleType",
        "library_nm": "Library_nM",
    }

    def _get_flowcell(self):
        # get the experiment name
        for line in self.section[self.HEADER]:
            if line[0] == "Experiment Name":
                return line[1]
        return None

    def _get_project_id(self):
        # get the experiment name
        for line in self.section[self.HEADER]:
            if line[0] == "Investigator Name":
                return line[1].split("_")[1]
        return None

    def massage(self, delim=",", end="\n"):
        """Abuses the Investigator Name field to store information about the run.

        Reshuffles the [Data] section so that it becomes a valid sample sheet.

        Returns a massaged SampleSheet.
        """
        # get the experiment name
        flowcell_id = self._get_flowcell()

        section_copy = deepcopy(self.section)

        for i, line in enumerate(section_copy[self.HEADER]):
            if line[0] == "Investigator Name":
                investigator_name = re.split(" |_", line[1])
                if investigator_name[-1] != flowcell_id:
                    investigator_name.append(flowcell_id)
                line[1] = "_".join(investigator_name)
                section_copy[self.HEADER][i] = line

        rs = []
        for section_marker, section in section_copy.items():
            if section_marker in self.section_markers:
                rs.append(delim.join(self.section_markers[section_marker]))
            for line in section:
                rs.append(delim.join(line))
        return end.join(rs)

    def to_demux(self, delim=",", end="\n"):
        """Replaced the [Data] section with a demuxable [Data] section.

        This is non destructive and will only return a demuxable samplesheet.

        Convert the Data section from
            Lane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,Sample_Project,Description,SampleType
        to
            FCID,Lane,SampleID,SampleRef,Index,Description,Control,Recipe,Operator,SampleProject
        """

        expected_header = [
            "FCID",
            "Lane",
            "SampleID",
            "SampleRef",
            "Index",
            "Description",
            "Control",
            "Recipe",
            "Operator",
            "SampleProject",
        ]

        # get the experiment name
        flowcell_id = self._get_flowcell()
        project_id = self._get_project_id()

        header = self.section[self.DATA][0]  # '0' is the csv header
        data_lines = (
            []
        )  # the new data section. Each line holds a dict with the right header keys
        data_lines.append(expected_header)
        for i, line in enumerate(self.section[self.DATA][1:]):
            data_line = dict(zip(header, line))

            data_line["FCID"] = flowcell_id
            data_line["SampleID"] = data_line["Sample_ID"]
            data_line["SampleRef"] = "hg19"
            data_line["Index"] = data_line["index"]
            data_line["Description"] = data_line["SampleType"]
            data_line["Control"] = project_id
            data_line["Recipe"] = "R1"
            data_line["Operator"] = "NN"
            data_line["SampleProject"] = project_id

            ordered_line = []
            for head in expected_header:
                ordered_line.append(data_line[head])
            data_lines.append(ordered_line)

        rs = []
        for line in data_lines:
            rs.append(delim.join(line))
        return end.join(rs)

Clinical-Genomics / demultiplexing / 921952146

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